The flora of Juncaceae from Bahia State, Brazil, is presented here. Four species of Juncus are recognised: J. densiflorus, J. marginatus, J. micranthus and J. microcephalus. This is the first report of J. marginatus in the Northeast Brazil; the species was previously known only from the South. An identification key, descriptions, illustrations, general notes and distribution maps of species in Bahia are provided.